Conserved intron positions in ancient protein modules

Background  

The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt) derived from GenBank.     

Population dynamics and life history tactics of arthropods from Mediterranean-type ecosystems

The null hypothesis of this paper is that survival of arthropods under the severe Mediterranean conditions involves specific combinations of conservative and conformist traits. To test this hypothesis a modeling approach employing a Leslie-type matrix model and a fuzzy systems technique for parameter estimation is developed and applied to a model species. The general conclusion is that the results of this paper add support to the null hypothesis, whereas specific conclusions are as follows: 1) matrix models merging demographic and physiological parameters are suitable tools for the simulation of population dynamics of arthropods and further for the discussion of the interplay among life history traits; 2) employing linguistic instead of arithmetic variables, fuzzy approaches allow for the formalization of incomplete and/or missing data exploiting expertise concerning related species; 3) in general, population dynamics of arthropods follow the seasonality of the Mediterranean climate; 4) the basic mechanism underlying skewing phenologies and stochastic equilibrium is identified with the type of temperature dependence of arthropod metabolic activity; 5) under optimal conditions an exponential trend is superimposed on seasonal population dynamics; 6) more realistic conditions involving large-scale random oscillation in temperature in autumn and spring coupled with small-scale temperature oscillation in summer and winter result in stochastic equilibrium; 7) moderate contamination of soil and medium-scale oscillation in temperature result in stable temporal patterns; 8) a sensitivity analysis shows disproportional effect of different demographic parameters on population growth rate. Fecundity of young and middle-aged adults is most important for the rate of population growth, whereas elder animals are considered an important pool for maintenance of the population.     

Sepsis progression and outcome: a dynamical model

Background  

Sepsis (bloodstream infection) is the leading cause of death in non-surgical intensive care units. It is diagnosed in 750,000 US patients per annum, and has high mortality. Current understanding of sepsis is predominately observational and correlational, with only a partial and incomplete understanding of the physiological dynamics underlying the syndrome. There exists a need for dynamical models of sepsis progression, based upon basic physiologic principles, which could eventually guide hourly treatment decisions.     

Membrane Curvature Induction and Tubulation Are Common Features of Synucleins and Apolipoproteins

Synucleins and apolipoproteins have been implicated in a number of membrane and lipid trafficking events. Lipid interaction for both types of proteins is mediated by 11 amino acid repeats that form amphipathic helices. This similarity suggests that synucleins and apolipoproteins might have comparable effects on lipid membranes, but this has not been shown directly. Here, we find that α-synuclein, β-synuclein, and apolipoprotein A-1 have the conserved functional ability to induce membrane curvature and to convert large vesicles into highly curved membrane tubules and vesicles. The resulting structures are morphologically similar to those generated by amphiphysin, a curvature-inducing protein involved in endocytosis. Unlike amphiphysin, however, synucleins and apolipoproteins do not require any scaffolding domains and curvature induction is mediated by the membrane insertion and wedging of amphipathic helices alone. Moreover, we frequently observed that α-synuclein caused membrane structures that had the appearance of nascent budding vesicles. The ability to function as a minimal machinery for vesicle budding agrees well with recent findings that α-synuclein plays a role in vesicle trafficking and enhances endocytosis. Induction of membrane curvature must be under strict regulation in vivo; however, as we find it can also cause disruption of membrane integrity. Because the degree of membrane curvature induction depends on the concerted action of multiple proteins, controlling the local protein density of tubulating proteins may be important. How cellular safeguarding mechanisms prevent such potentially toxic events and whether they go awry in disease remains to be determined.     

Quantifying nature: ideological representations in the concept of diversity

The conflicts around the scientific status of the concept of diversity are considered here as symptoms of hidden, socially originated, ideological representations inherent in the theoretical context of western ecology. Species diversity was coined in the 1940s, as a constant in the statistical models that described the distribution of individuals into different species and, therefore, as the expression of all the parameters that determine ecologically this distribution. The assumption of such a regular distribution is attributed to the influence of organicism and the correlated presuppositions of harmony and homeostasis. Nevertheless, as species diversity was the only unknown parameter in these models, it reversed the direction of the functions and established itself as the main variable under question. After the 1950s, the concept of species diversity was empowered by the strong impact of cybernetics and systems theories; in this context, diversity was considered as a self-regulating mechanism that assures overall stability. Diversity emerges as a natural and one-dimensional measure of community complexity, maturity, and stability. In the perspective of the arising ecological crisis, diversity--because of its property to compare and evaluate--arises as the nodal point of the new scientific/ideological fields of nature conservation and ecosystem management.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.     

Amphipathic motifs in BAR domains are essential for membrane curvature sensing

BAR (Bin/Amphiphysin/Rvs) domains and amphipathic α‐helices (AHs) are believed to be sensors of membrane curvature thus facilitating the assembly of protein complexes on curved membranes. Here, we used quantitative fluorescence microscopy to compare the binding of both motifs on single nanosized liposomes of different diameters and therefore membrane curvature. Characterization of members of the three BAR domain families showed surprisingly that the crescent‐shaped BAR dimer with its positively charged concave face is not able to sense membrane curvature. Mutagenesis on BAR domains showed that membrane curvature sensing critically depends on the N‐terminal AH and furthermore that BAR domains sense membrane curvature through hydrophobic insertion in lipid packing defects and not through electrostatics. Consequently, amphipathic motifs, such as AHs, that are often associated with BAR domains emerge as an important means for a protein to sense membrane curvature. Measurements on single liposomes allowed us to document heterogeneous binding behaviour within the ensemble and quantify the influence of liposome polydispersity on bulk membrane curvature sensing experiments. The latter results suggest that bulk liposome‐binding experiments should be interpreted with great caution.     

Analysis of the distribution of epiphytic lichens within homogeneousFagus sylvatica stands along an altitudinal gradient (Mount Olympos,Greece)

Epiphytic lichen vegetation onFagus sylvatica sas studied in 4 sites along an altitudinal gradient from 930 to 1500 m on SE facing slopes of Mount Olympos (Greece). The crucial factor determining the spatial heterogeneity of epiphytic lichens onF. sylvatica is the altitude and not the height on the trunk at which lichen community is established. 17 out of 26 taxa are confined to a particular elevation range, while another three are clearly ubiquitous in their distribution. The number of lichen species at breast height is higher than at the base of the trunks. The results were compared with those gathered earlier in an analogous study on the vertical distribution of epiphytic lichens onPinus nigra along an altitudinal gradient from 750 to 1510 m of the same mountain. Comparison suggests that spatial heterogeneity of epiphytic lichens onF. sylvatica is different from the one onP. nigra.